Affiliation

Abstract

Complete folding is not a prerequisite for protein function, as disordered and partially folded states of proteins frequently perform essential biological functions. In order to understand their functions at the molecular level, we utilized diverse experimental measurements to calculate ensemble models of three nonhomologous, intrinsically disordered proteins: I-2, spinophilin, and DARPP-32, which bind to and regulate protein phosphatase 1 (PP1). The models demonstrate that these proteins have dissimilar propensities for secondary and tertiary structure in their unbound forms. Direct comparison of these ensemble models with recently determined PP1 complex structures suggests a significant role for transient, preformed structure in the interactions of these proteins with PP1. Finally, we generated an ensemble model of partially disordered I-2 bound to PP1 that provides insight into the relationship between flexibility and biological function in this dynamic complex.

Figures

Secondary structure content of calculated ensembles for (a) I-29–164, (b) spinophilin417–494 and (c) DARPP-321–118. Lines represent the α-helix populations (green), populations in the broad α (blue), left-β (red) and right-β (purple) regions of the Ramachandran diagram. All values are plotted with a three-residue smoothing. Secondary structures observed in the bound-state crystal structures of I-2 and spinophilin are shown above the plots with α-helices in green, βstrands in red and other observed regions in blue.

Significantly populated clusters and their fractional contact plots for (a) I-29–164, (b) spinophilin417–494 and (c) DARPP-321–118. Fractional contact plots represent the fractional formation of contacts between pairs of residues, with a contact being defined as any two heavy atoms being within 10 Å of each other. The upper halves of the contact plots show contacts present in the clusters while the lower halves show contacts present in PP1-bound I-2 and spinophilin. White represents regions not present in the PP1-bound structures, either as no electron density was detected or because different construct lengths were used in the studies. Structures are colored as follows: I-2 – residues 6–58 red, 59–111 green, 112–164 blue; spinophilin – residues 417–442 red, 443–468 green, 469–494 blue; DARPP-32 – residues 1–39 red, 40–78 green, 79–118 blue. See also Table S1.

Figure 3

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PP1:I-2 NMR study. (a) 2D…

Figure 3

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PP1:I-2 NMR study. (a) 2D [ 1 H, 15 N] HSQC/TROSY spectra of…

Figure 3

PP1:I-2 NMR study. (a) 2D [1H,15N] HSQC/TROSY spectra of unbound 15N-labeled I-29–164 (black) and 15N,2H-labeled I-29–164 in complex with unlabeled PP1 (red). Spectra were aligned by overlaying the peaks belonging to the Nε1 of Trp46. (b) Chemical shift changes in I-29–164 upon addition of PP1 are small and are primarily localized to regions observed in the crystal structure of the bound complex. The chemical shift differences (Δδ) between peaks in unbound and bound spectra were calculated as
(ΔδH)2+(ΔδN10)2.

Figure 4

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The PP1:I-2 complex. (a) PP1…

Figure 4

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The PP1:I-2 complex. (a) PP1 is shown in a grey surface representation while…

Figure 4

The PP1:I-2 complex. (a) PP1 is shown in a grey surface representation while I-2 is shown in various colors: the region observed in the PP1:I-2 crystal structure is shown in light blue while the three disordered regions of I-2, residues 6–10, 17–41 and 55–127, are colored orange, green and red, respectively. Thr72 is shown in black. (b) Fitting of the PP1:I-2 complex model into the crystallographic unit cell. The most extended conformer of the PP1:I-2 complex model was overlaid with the PP1:I-2 crystal structure, and unit cell information from the crystal structure was applied to the complex model. Symmetry mates were then added to determine whether the PP1:I-2 model fits into the crystallographic unit cell. (c) Fractional contact plots for the unbound I-2 ensembles (top left) and the PP1-bound I-2 ensemble model (bottom right). The color scale is the same as in Figure 2.

Figure 5

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SAXS data and analysis for…

Figure 5

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SAXS data and analysis for the PP1:I-2 complex. (a) The Guinier region of…

Figure 5

SAXS data and analysis for the PP1:I-2 complex. (a) The Guinier region of the scattering curve for 0.8 mg/ml and 0.5 mg/ml PP1:I-2. (b) Average theoretical scattering curve for the ensemble models (red line) fit to the experimental scattering data for PP1:I-2 (squares). (c) Overlay of the SAXS envelope (surface representation, blue) with the PP1:I-2 ensemble models. PP1 is shown as a cartoon representation in black and I-2 is shown as a cartoon representation in red. See also Figure S8.